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Article ; Online: Molecular Basis of the Toxigenic Vibrio cholerae O1 Serotype Switch from Ogawa to Inaba in Haiti.

Paisie, Taylor K / Cash, Melanie N / Tagliamonte, Massimiliano S / Ali, Afsar / Morris, J Glenn / Salemi, Marco / Mavian, Carla

Microbiology spectrum

2022 Volume 11, Issue 1, Page(s) e0362422

Abstract: Toxigenic Vibrio cholerae O1 serotype Ogawa was introduced involuntarily into Haiti in October 2010, and virtually all of the clinical strains isolated during the first 5 years of the epidemic were Ogawa. Inaba strains were identified intermittently ... ...

Abstract	Toxigenic Vibrio cholerae O1 serotype Ogawa was introduced involuntarily into Haiti in October 2010, and virtually all of the clinical strains isolated during the first 5 years of the epidemic were Ogawa. Inaba strains were identified intermittently prior to 2015, with diverse mutations resulting in a common phenotype. In 2015, the percentage of clinical infections due to the Inaba serotype began to rapidly increase, with Inaba supplanting Ogawa as the dominant serotype during the subsequent 4 years. We investigated the molecular basis of the serotype switch and confirmed that all Inaba strains had the same level of mRNA expression of the
MeSH term(s)	Humans ; Vibrio cholerae O1/genetics ; Serogroup ; Cholera/epidemiology ; Haiti/epidemiology ; Serotyping
Language	English
Publishing date	2022-12-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.03624-22
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Article ; Online: UBASH3A Regulates the Synthesis and Dynamics of TCR-CD3 Complexes.

Ge, Yan / Paisie, Taylor K / Chen, Sixue / Concannon, Patrick

Journal of immunology (Baltimore, Md. : 1950)

2019 Volume 203, Issue 11, Page(s) 2827–2836

Abstract: The TCR-CD3 complex is a multicomponent membrane receptor, the expression of which is tightly regulated in thymocytes, as well as in mature T cells both at steady state and upon stimulation. In this study, we report novel roles for UBASH3A in TCR-CD3 ... ...

Abstract	The TCR-CD3 complex is a multicomponent membrane receptor, the expression of which is tightly regulated in thymocytes, as well as in mature T cells both at steady state and upon stimulation. In this study, we report novel roles for UBASH3A in TCR-CD3 synthesis and turnover. UBASH3A is a negative regulator of T cell function and plays a broad role in autoimmunity. We show that modulation of UBASH3A levels in unstimulated Jurkat cells leads to altered amounts of total cellular CD3 chains and of cell-surface TCR-CD3 complexes; in contrast, UBASH3A does not affect the level of cell-surface CD28, an important T cell costimulatory receptor. Upon TCR engagement, UBASH3A enhances the downmodulation of cell-surface TCR-CD3. Mass spectrometry and protein-protein interaction studies uncover novel associations between UBASH3A and components of several cellular pathways involved in the regulation of TCR-CD3 turnover and dynamics, including endoplasmic reticulum-associated protein degradation, cell motility, endocytosis, and endocytic recycling of membrane receptors. Finally, we demonstrate that the SH3 domain of UBASH3A mediates its binding to CBL-B, an E3 ubiquitin ligase that negatively regulates CD28-mediated signaling and, hence, T cell activation. In summary, this study provides new mechanistic insights into how UBASH3A regulates T cell activation and contributes to autoimmunity. The interaction between UBASH3A and CBL-B may synergistically inhibit T cell function and affect risk for type 1 diabetes, as both genes have been shown to be associated with this autoimmune disease.
MeSH term(s)	Adaptor Proteins, Signal Transducing/deficiency ; Adaptor Proteins, Signal Transducing/immunology ; CD3 Complex/immunology ; Cells, Cultured ; HEK293 Cells ; Humans ; Jurkat Cells ; Receptors, Antigen, T-Cell/immunology
Chemical Substances	Adaptor Proteins, Signal Transducing ; CD3 Complex ; Receptors, Antigen, T-Cell ; UBASH3A protein, human
Language	English
Publishing date	2019-10-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	3056-9
ISSN	1550-6606 ; 0022-1767 ; 1048-3233 ; 1047-7381
ISSN (online)	1550-6606
ISSN	0022-1767 ; 1048-3233 ; 1047-7381
DOI	10.4049/jimmunol.1801338
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Article ; Online: Emergence and Evolutionary Response of Vibrio cholerae to Novel Bacteriophage, Democratic Republic of the Congo

Alam, Meer T / Mavian, Carla / Paisie, Taylor K / Tagliamonte, Massimiliano S / Cash, Melanie N / Angermeyer, Angus / Seed, Kimberley D / Camilli, Andrew / Maisha, Felicien Masanga / Senga, R Kabangwa Kakongo / Salemi, Marco / Morris, J Glenn / Ali, Afsar

Emerging infectious diseases

2022 Volume 28, Issue 12, Page(s) 2482–2490

Abstract: Cholera causes substantial illness and death in Africa. We analyzed 24 toxigenic Vibrio cholerae O1 strains isolated in 2015-2017 from patients in the Great Lakes region of the Democratic Republic of the Congo. Strains originating in southern Asia ... ...

Abstract	Cholera causes substantial illness and death in Africa. We analyzed 24 toxigenic Vibrio cholerae O1 strains isolated in 2015-2017 from patients in the Great Lakes region of the Democratic Republic of the Congo. Strains originating in southern Asia appeared to be part of the T10 introduction event in eastern Africa. We identified 2 main strain lineages, most recently a lineage corresponding to sequence type 515, a V. cholerae cluster previously reported in the Lake Kivu region. In 41% of fecal samples from cholera patients, we also identified a novel ICP1 (Bangladesh cholera phage 1) bacteriophage, genetically distinct from ICP1 isolates previously detected in Asia. Bacteriophage resistance occurred in distinct clades along both internal and external branches of the cholera phylogeny. This bacteriophage appears to have served as a major driver for cholera evolution and spread, and its appearance highlights the complex evolutionary dynamic that occurs between predatory phage and bacterial host.
MeSH term(s)	Humans ; Cholera/epidemiology ; Cholera/microbiology ; Bacteriophages/genetics ; Democratic Republic of the Congo/epidemiology ; Vibrio cholerae O1 ; Phylogeny
Language	English
Publishing date	2022-11-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2812.220572
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Article ; Online: Effects of a ciliate protozoa predator on microbial communities in pitcher plant (Sarracenia purpurea) leaves.

Paisie, Taylor K / Miller, Thomas E / Mason, Olivia U

PloS one

2014 Volume 9, Issue 11, Page(s) e113384

Abstract: The aquatic communities found within the water filled leaves of the pitcher plant, Sarracenia purpurea, have a simple trophic structure providing an ideal system to study microscale interactions between protozoan predators and their bacterial prey. In ... ...

Abstract	The aquatic communities found within the water filled leaves of the pitcher plant, Sarracenia purpurea, have a simple trophic structure providing an ideal system to study microscale interactions between protozoan predators and their bacterial prey. In this study, replicate communities were maintained with and without the presence of the bactivorous protozoan, Colpoda steinii, to determine the effects of grazing on microbial communities. Changes in microbial (Archaea and Bacteria) community structure were assessed using iTag sequencing of 16S rRNA genes. The microbial communities were similar with and without the protozoan predator, with>1000 species. Of these species, Archaea were negligible, with Bacteria comprising 99.99% of the microbial community. The Proteobacteria and Bacteroidetes were the most dominant phyla. The addition of a protozoan predator did not have a significant effect on microbial evenness nor richness. However, the presence of the protozoan did cause a significant shift in the relative abundances of a number of bacterial species. This suggested that bactivorous protozoan may target specific bacterial species and/or that certain bacterial species have innate mechanisms by which they evade predators. These findings help to elucidate the effect that trophic structure perturbations have on predator prey interactions in microbial systems.
MeSH term(s)	Archaea/genetics ; Archaea/isolation & purification ; Bacteria/genetics ; Bacteria/isolation & purification ; Ciliophora/growth & development ; Ciliophora/parasitology ; Plant Leaves/microbiology ; Plant Leaves/parasitology ; RNA, Ribosomal, 16S/genetics ; Sarraceniaceae/microbiology ; Sarraceniaceae/parasitology
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2014
Publishing country	United States
Document type	Journal Article
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0113384
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Article ; Online: UBASH3A Mediates Risk for Type 1 Diabetes Through Inhibition of T-Cell Receptor-Induced NF-κB Signaling.

Ge, Yan / Paisie, Taylor K / Newman, Jeremy R B / McIntyre, Lauren M / Concannon, Patrick

Diabetes

2017 Volume 66, Issue 7, Page(s) 2033–2043

Abstract: Although over 40 type 1 diabetes (T1D) risk loci have been mapped in humans, the causative genes and variants for T1D are largely unknown. Here, we investigated a candidate gene in the 21q22.3 risk locus- ...

Abstract	Although over 40 type 1 diabetes (T1D) risk loci have been mapped in humans, the causative genes and variants for T1D are largely unknown. Here, we investigated a candidate gene in the 21q22.3 risk locus-
MeSH term(s)	Adaptor Proteins, Signal Transducing/genetics ; Adaptor Proteins, Signal Transducing/immunology ; CD4-Positive T-Lymphocytes ; Diabetes Mellitus, Type 1/genetics ; Diabetes Mellitus, Type 1/immunology ; Enzyme-Linked Immunosorbent Assay ; Gene Knockout Techniques ; Genetic Predisposition to Disease ; HEK293 Cells ; Humans ; I-kappa B Kinase/immunology ; Interleukin-2/genetics ; Interleukin-2/immunology ; Jurkat Cells ; Leukocytes, Mononuclear/immunology ; MAP Kinase Kinase Kinases/immunology ; NF-kappa B/immunology ; Polymerase Chain Reaction ; Receptors, Antigen, T-Cell/immunology ; Signal Transduction/genetics ; Signal Transduction/immunology ; Ubiquitin/immunology
Chemical Substances	Adaptor Proteins, Signal Transducing ; IKBKG protein, human ; IL2 protein, human ; Interleukin-2 ; NF-kappa B ; Receptors, Antigen, T-Cell ; UBASH3A protein, human ; Ubiquitin ; I-kappa B Kinase (EC 2.7.11.10) ; MAP Kinase Kinase Kinases (EC 2.7.11.25) ; MAP kinase kinase kinase 7 (EC 2.7.11.25)
Language	English
Publishing date	2017-06-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80085-5
ISSN	1939-327X ; 0012-1797
ISSN (online)	1939-327X
ISSN	0012-1797
DOI	10.2337/db16-1023
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Article: Mississippi River Plume Enriches Microbial Diversity in the Northern Gulf of Mexico.

Mason, Olivia U / Canter, Erin J / Gillies, Lauren E / Paisie, Taylor K / Roberts, Brian J

Frontiers in microbiology

2016 Volume 7, Page(s) 1048

Abstract: The Mississippi River (MR) serves as the primary source of freshwater and nutrients to the northern Gulf of Mexico (nGOM). Whether this input of freshwater also enriches microbial diversity as the MR plume migrates and mixes with the nGOM serves as the ... ...

Abstract	The Mississippi River (MR) serves as the primary source of freshwater and nutrients to the northern Gulf of Mexico (nGOM). Whether this input of freshwater also enriches microbial diversity as the MR plume migrates and mixes with the nGOM serves as the central question addressed herein. Specifically, in this study physicochemical properties and planktonic microbial community composition and diversity was determined using iTag sequencing of 16S rRNA genes in 23 samples collected along a salinity (and nutrient) gradient from the mouth of the MR, in the MR plume, in the canyon, at the Deepwater Horizon wellhead and out to the loop current. Analysis of these datasets revealed that the MR influenced microbial diversity as far offshore as the Deepwater Horizon wellhead. The MR had the highest microbial diversity, which decreased with increasing salinity. MR bacterioplankton communities were distinct compared to the nGOM, particularly in the surface where Actinobacteria and Proteobacteria dominated, while the deeper MR was also enriched in Thaumarchaeota. Statistical analyses revealed that nutrients input by the MR, along with salinity and depth, were the primary drivers in structuring the microbial communities. These results suggested that the reduced salinity, nutrient enriched MR plume could act as a seed bank for microbial diversity as it mixes with the nGOM. Whether introduced microorganisms are active at higher salinities than freshwater would determine if this seed bank for microbial diversity is ecologically significant. Alternatively, microorganisms that are physiologically restricted to freshwater habitats that are entrained in the plume could be used as tracers for freshwater input to the marine environment.
Language	English
Publishing date	2016-07-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2016.01048
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Article ; Online: Toxigenic

Mavian, Carla / Paisie, Taylor K / Alam, Meer T / Browne, Cameron / Beau De Rochars, Valery Madsen / Nembrini, Stefano / Cash, Melanie N / Nelson, Eric J / Azarian, Taj / Ali, Afsar / Morris, J Glenn / Salemi, Marco

Proceedings of the National Academy of Sciences of the United States of America

2020 Volume 117, Issue 14, Page(s) 7897–7904

Abstract: The spread of cholera in the midst of an epidemic is largely driven by direct transmission from person to person, although it is well-recognized ... ...

Abstract	The spread of cholera in the midst of an epidemic is largely driven by direct transmission from person to person, although it is well-recognized that
MeSH term(s)	Asia/epidemiology ; Cholera/epidemiology ; Cholera/genetics ; Cholera/microbiology ; Cholera/pathology ; Disease Outbreaks ; Ecosystem ; Genome, Bacterial/genetics ; Haiti/epidemiology ; Humans ; Phylogeny ; Vibrio cholerae O1/classification ; Vibrio cholerae O1/genetics ; Vibrio cholerae O1/pathogenicity ; Water Microbiology
Language	English
Publishing date	2020-03-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1918763117
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Article ; Online: Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.

Mavian, Carla / Pond, Sergei Kosakovsky / Marini, Simone / Magalis, Brittany Rife / Vandamme, Anne-Mieke / Dellicour, Simon / Scarpino, Samuel V / Houldcroft, Charlotte / Villabona-Arenas, Julian / Paisie, Taylor K / Trovão, Nídia S / Boucher, Christina / Zhang, Yun / Scheuermann, Richard H / Gascuel, Olivier / Lam, Tommy Tsan-Yuk / Suchard, Marc A / Abecasis, Ana / Wilkinson, Eduan /

de Oliveira, Tulio / Bento, Ana I / Schmidt, Heiko A / Martin, Darren / Hadfield, James / Faria, Nuno / Grubaugh, Nathan D / Neher, Richard A / Baele, Guy / Lemey, Philippe / Stadler, Tanja / Albert, Jan / Crandall, Keith A / Leitner, Thomas / Stamatakis, Alexandros / Prosperi, Mattia / Salemi, Marco

Proceedings of the National Academy of Sciences of the United States of America

2020 Volume 117, Issue 23, Page(s) 12522–12523

MeSH term(s)	Betacoronavirus ; COVID-19 ; Coronavirus Infections ; Humans ; Pandemics ; Phylogeny ; Pneumonia, Viral ; Severe acute respiratory syndrome-related coronavirus ; SARS-CoV-2 ; Selection Bias
Keywords	covid19
Language	English
Publishing date	2020-05-07
Publishing country	United States
Document type	Letter ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Comment
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2007295117
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Article: Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

Proc Natl Acad Sci U S A

Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #32381734
Database	COVID19

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Article ; Online: Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.

2020

Abstract: There is obvious interest in gaining insights into the epidemiology and evolution of the virus that has recently emerged in humans as the cause of the coronavirus disease 2019 (COVID-19) pandemic. The recent paper by Forster et al. (1), analyzed 160 SARS- ...

Abstract	There is obvious interest in gaining insights into the epidemiology and evolution of the virus that has recently emerged in humans as the cause of the coronavirus disease 2019 (COVID-19) pandemic. The recent paper by Forster et al. (1), analyzed 160 SARS-CoV-2 full genomes available (https://www.gisaid.org/) in early March 2020. The central claim is the identification of three main SARS-CoV-2 types, named A, B, and C, circulating in different proportions among Europeans and Americans (types A and C) and East Asian (type B). According to a median-joining network analysis, variant A is proposed to be the ancestral type because it links to the sequence of a coronavirus from bats, used as an outgroup to trace the ancestral origin of the human strains. The authors further suggest that the “ancestral Wuhan B-type virus is immunologically or environmentally adapted to a large section of the East Asian population, and may need to mutate to overcome resistance outside East Asia”. There are several serious flaws with their findings and interpretation. First, and most obviously, the sequence identity between SARS-CoV-2 and the bat virus is only 96.2%, implying that these viral genomes (which are nearly 30,000 nucleotides long) differ by more than 1,000 mutations. Such a distant outgroup is unlikely to provide a reliable root for the network. Yet, strangely, the branch to the bat virus, in Figure 1 of the paper, is only 16 or 17 mutations in length. Indeed, the network seems to be mis-rooted because (see Supplementary Figure 4) a virus from Wuhan from week 0 (24th December 2019) is portrayed as a descendant of a clade of viruses collected in weeks 1-9 (presumably from many places outside China), which makes no evolutionary (2), nor epidemiological sense (3). NA
Keywords	Humans ; SARS Virus ; Pneumonia ; Viral ; Coronavirus Infections ; Selection Bias ; Phylogeny ; Pandemics ; Betacoronavirus ; covid19
Language	English
Publisher	National Academy of Sciences
Publishing country	uk
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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